Seg2Dgel
Class Sg2dbug

java.lang.Object
  Seg2Dgel.Sg2glb
      Seg2Dgel.Sg2dbug

public class Sg2dbug
extends Sg2glb

Class Sg2dbug contains debug print methods for image neighbohood, windows, etc. used by the 2D Gel Spot Segmenter Seg2Dgel. This class contains methods for reading and parsing the Seg2Dgel.dbug name/bits file for use in print out the debug bits list if the -debug switch was invoked.

This code was derived and refactored from GELLAB-II sg2gii C language files.

This work was produced by Peter Lemkin of the National Cancer Institute, an agency of the United States Government. As a work of the United States Government there is no associated copyright. It is offered as open source software under the Mozilla Public License (version 1.1) subject to the limitations noted in the accompanying LEGAL file. This notice must be included with the code. The Open2Dprot Mozilla and Legal files are available on http://Open2Dprot.sourceforge.net/.

Version:

$Date: 2005/10/21 17:08:03 $ $Revision: 1.19 $

Author:

P. Lemkin, NCI-Frederick, Frederick, MD, 21702

See Also:

Open2Dprot Home

Field Summary

static java.lang.String[]	dbugBitName Debug bits name from the parsed Seg2Dgel.dbug file
static int[]	dbugBitValues Debug bits values from the parsed Seg2Dgel.dbug file

Fields inherited from class Seg2Dgel.Sg2glb

acc, accDatabaseFile, accDatabaseSwitch, accFile, accFormatMode, allowTouchingEdgesSwitch, applicationName, argsV, averageODSwitch, avg, avgPixFile, banner, bannerTitle, baseImageFileName, baseStatusTime, batchDir, bfav, bfavm, bfavm1, bfavp, bfavp1, bfog, bfogm, bfogm1, bfogm2, bfogm3, bfogm4, bfogm5, bfogp, bfogp1, bfogp2, bfogp3, bfogp4, bfogp5, bkg, BKGRD_CODE, bkgrdCorrectionSwitch, bkgrdPixFile, bkgrdSizeFlag, BLACK, boundaryInSSFSwitch, bufbkg, bufcc, bufmag, bufrest, c11, c12, c13, c14, c15, c16, c17, c18, c19, c1a, c1b, c1c, c1d, c1e, c1f, c1g, c1h, c21, c22, c23, c24, c25, c26, c27, c28, c29, c2a, c2b, c2c, c2d, c2e, c2f, c2g, c2h, c31, c32, c33, c34, c35, c36, c37, c38, c39, c3a, c3b, c3c, c3d, c3e, c3f, c3g, c3h, c41, c42, c43, c44, c45, c46, c47, c48, c49, c4a, c4b, c4c, c4d, c4e, c4f, c4g, c4h, c51, c52, c53, c54, c55, c56, c57, c58, c59, c5a, c5b, c5c, c5d, c5e, c5f, c5g, c5h, c61, c62, c63, c64, c65, c66, c67, c68, c69, c6a, c6b, c6c, c6d, c6e, c6f, c6g, c6h, c71, c72, c73, c74, c75, c76, c77, c78, c79, c7a, c7b, c7c, c7d, c7e, c7f, c7g, c7h, c81, c82, c83, c84, c85, c86, c87, c88, c89, c8a, c8b, c8c, c8d, c8e, c8f, c8g, c8h, c91, c92, c93, c94, c95, c96, c97, c98, c99, c9a, c9b, c9c, c9d, c9e, c9f, c9g, c9h, ca1, ca2, ca3, ca4, ca5, ca6, ca7, ca8, ca9, caa, cab, cac, cacheDir, cad, cae, caf, cag, cah, cal, cal2gray, calFile, cb1, cb2, cb3, cb4, cb5, cb6, cb7, cb8, cb9, cba, cbb, cbc, cbd, cbe, cbf, cbg, cbh, cc, cc1, cc2, cc3, cc4, cc5, cc6, cc7, cc8, cc9, cca, ccb, ccc, ccd, cce, ccf, ccg, cch, ccMinSize, ccMinSizeSwitch, ccNum, ccPixFile, cd1, cd2, cd3, cd4, cd5, cd6, cd7, cd8, cd9, cda, cdb, cdc, cdd, cde, cdf, cdg, cdh, computingWindowSwitch, coneOfSilenceMode, CONSOLE_FLAG, ctlCorePixSwitch, cwx1, cwx2, cwy1, cwy2, data, DATE, dbSample, dbSpot, dbug, DBUG_ADD_INTERIOR_CC_PIXELS, DBUG_BND_ANALYSIS, DBUG_CALC_FEATURES, DBUG_CHAIN_CODE_RLM_ANALYSIS, DBUG_CONSOLE, DBUG_CVT_BND_TO_CHAINCODE, DBUG_DRAW_NOTCH_PAIR_LINE, DBUG_DRAW_SAT_SPOT_BND, DBUG_DUMP_CC_PPX, DBUG_FILL_CORNERS, DBUG_FILL_HOLES_IN_PCC_CONCAVITIES, DBUG_FIND_BND_NOTCHES_IN_CHAIN_CODE, DBUG_FIND_SPOT_LIST, DBUG_INNER_LOOP_FIND_SPOT, DBUG_MAX_PROPAGATE, DBUG_NBR_COMPONENTS, DBUG_PIX_DBCODE, DBUG_PRINT_GRAY2CAL_MAP, DBUG_PROP_SAT_SPOTS, DBUG_PROP_SPOT_TO_2ND_MAXIMA, DBUG_PUSH_XY_INTO_FBL, DBUG_RMV_CONCAVITIES, DBUG_RMV_INTERIOR_CC_PIXELS, DBUG_ROUND_CORNERS, DBUG_SPLIT_CHECK_SPOT, DBUG_SPLIT_PIX_BY_FBL_BND_ANALSIS, DBUG_SWITCHES, dbugBits, dbugBitsHelpStr, dbugBitsPixFlag, dbx1, dbx2, dby1, dby2, debugSwitch, defaultSwitch, defaultTypeCode, deleteIsolatedPixelsSwitch, demoFileList, demoSwitch, DFT_2D_GEL, DFT_2D_LC_MS, DFT_NO_DB, didPropSaturatedSpots, didSplitSpotFlag, diffODSwitch, docFileList, dotsSwitch, dpx1, dpx2, dpy1, dpy2, draw, drawBoundaryOverlayType, drawBoundarySwitch, drawDotOverlayType, drawMEROverlayType, drawMERSwitch, drawPlusOverlayType, drawPlusSwitch, drawSxSyEllipseSwitch, drawSxSyOverlayType, drawTitleSwitch, dtdSwitch, ENABLE_DEVELOPER_DEBUGGING, ENABLE_SATURATED_SPOTS, ENABLE_SPOT_SPLITTING, fbl, fileSeparator, fio, fnd, fourSqrtPi, gHist, glbPercentThr, gray2cal, gridSize, hashFBL, HASHFBLPRIME, hashWS, histThreshold, i0R, i10, i11, i12, i13, i14, i15, i16, i17, i18, i2U, i4L, i6D, ini, inPixFile, ISOLATED_PIXEL_CODE, j11, j12, j13, j14, j15, j16, j17, j18, j19, j1a, j1b, j1c, j1d, j1e, j1f, j1g, j1h, j21, j22, j23, j24, j25, j26, j27, j28, j29, j2a, j2b, j2c, j2d, j2e, j2f, j2g, j2h, j31, j32, j33, j34, j35, j36, j37, j38, j39, j3a, j3b, j3c, j3d, j3e, j3f, j3g, j3h, j41, j42, j43, j44, j45, j46, j47, j48, j49, j4a, j4b, j4c, j4d, j4e, j4f, j4g, j4h, j51, j52, j53, j54, j55, j56, j57, j58, j59, j5a, j5b, j5c, j5d, j5e, j5f, j5g, j5h, j61, j62, j63, j64, j65, j66, j67, j68, j69, j6a, j6b, j6c, j6d, j6e, j6f, j6g, j6h, j71, j72, j73, j74, j75, j76, j77, j78, j79, j7a, j7b, j7c, j7d, j7e, j7f, j7g, j7h, j81, j82, j83, j84, j85, j86, j87, j88, j89, j8a, j8b, j8c, j8d, j8e, j8f, j8g, j8h, j91, j92, j93, j94, j95, j96, j97, j98, j99, j9a, j9b, j9c, j9d, j9e, j9f, j9g, j9h, ja1, ja2, ja3, ja4, ja5, ja6, ja7, ja8, ja9, jaa, jab, jac, jad, jae, jaf, jag, jah, jarFileList, jarLibrFileList, jb1, jb2, jb3, jb4, jb5, jb6, jb7, jb8, jb9, jba, jbb, jbc, jbd, jbe, jbf, jbg, jbh, jc1, jc2, jc3, jc4, jc5, jc6, jc7, jc8, jc9, jca, jcb, jcc, jcd, jce, jcf, jcg, jch, jd1, jd2, jd3, jd4, jd5, jd6, jd7, jd8, jd9, jda, jdb, jdc, jdd, jde, jdf, jdg, jdh, keepInputImageSwitch, KILL_SPOT_CODE, killSpotColor, laplacianSwitch, legalImageFileExtens, lineLaplacianHeight, lineLaplacianWidth, lowPassSize, lowpassSwitch, lp13xZZSwitch, lp3x3Switch, lp5x5Switch, lp7x7Switch, mag2ndPixFile, MAX_BUFFERED_SPOTS, MAX_CC_CODE, MAX_INTERIOR_FBL_SIZE, MAX_PCC_CODE, maxColsToPrint, maxGhist, maxGrayPixel, MAXSUBSPOTS, meanGhist, merx1, merx2, merxp1, merxp2, mery1, mery2, meryp1, meryp2, MHISTSIZE, MIN_CC_CODE, MIN_PCC_CODE, MINBLOBAREA, minGhist, MINSPLITSPOTSIZE, nBitsPerPixel, nBkgrdSize, nBytesPerPixel, NEVER, ngh, notch, nPixels, nStatusName, nSwitches, optimizeInteriorFBLSwitch, osName, paramH, PCC_BASE_CODE, pix, pix1, pix2, pix3, pix4, pix5, pix6, pix7, pixDir, pixDumpSwitch, pixelSizeMicrons, pixFileExtn, pixHeight, pixWidth, ppxDir, pra, projDir, projDirSwitch, propertiesFile, propertiesFileSwitch, pTileGhist, PUBLISH, quickEstimateSwitch, rdbmsDir, rest, restOfPixFile, restOfPixSwitch, REVISION, rlmCWfile, rmvDprimeSizingSwitch, sampleSwitch, sat, saturatedSpotSwitch, scaledMaxOD, seg2dgelURL, segPixFile, segPixSwitch, sg2, simpleFileName, sizeFractionGaussianWidth, sort, split, splitLargeCCfblByBndAnalSwitch, splitLargeCCfblByRLManalSwitch, splitLargeCCfblByThreshAnalSwitch, splitMinCCsize, splitSpotSwitch, spotNumber, ssfFormatMode, ssfFormatSwitch, ssfOutputEpilogueFile, ssfOutputFile, ssfOutputPrefaceFile, startTime, statusMemoryFree, statusMemoryTot, statusName, statusStartTime, sw, switchOptCBvalue, switchOptData, switchOptValue, t1Area, t1Density, t1Range, t1SxSyRatio, t2Area, t2Density, t2Range, t2SxSyRatio, TEST_LARGE_IMAGE, thrAreaSwitch, thrDensitySwitch, thrRangeSwitch, thrSxSyRatioSwitch, timerSwitch, tmpDir, UNLABELED_CC_CODE, updateSwitch, usageSwitch, USE_13X13, USE_BKGD_AND_ISOLATED_PIXEL_BACKGROUND, USE_DEMO_DATA, USE_DOM_XML_SSF, use3x3laplacianSwitch, use5x5laplacianSwitch, useBkgdAndIsolatedPixelFlag, useBusseLaplacianSwitch, useCopyOfPix1ForPix5Switch, useHistGUISwitch, useHorizLineLaplacianSwitch, usePopupGUISwitch, userDir, useVertLineLaplacianSwitch, util, VERSION, WHITE, widthWindmp, windmpStepSize, wrk, wXsize, wYsize, xDbug, xmlDir, xPentrance, xPexit, yDbug, yPentrance, yPexit, yTitle

Constructor Summary

Sg2dbug()
Sg2dbug() - Constructor

Method Summary

static void	dbugPixDBcode(char[] pix, int radixMode, java.lang.String title) dbugPixDBcode() - print window of current char[] picture if enabled by dbugBitsPixFlag and (xDbug,yDbug) is inside of [dpx1:dpx2,dpy1:dpy2].
static void	dbugPixDBcode(char[] pix, java.lang.String title) dbugPixDBcode() - print window of current char[] picture if enabled by dbugBitsPixFlag and (xDbug,yDbug) is inside of [dpx1:dpx2,dpy1:dpy2].
static void	dbugPixNxNcode(char[] pix, int x, int y, int n, java.lang.String title) dbugPixNxNcode() - print window of size (n X n) of current char[] picture if enabled by dbugBitsPixFlag and (xDbug,yDbug) is inside of [dbx1:dbx2, dby1:dby2] to ssfFD.
static void	pixDump(char[] pix, int radixMode, java.lang.String title) pixDump() - print window of current 16-bit char[] picture if pixDumpSwitch is enabled.
static void	pixDump(char[] pix, java.lang.String title) pixDump() - print window of current 16-bit char[] picture if pixDumpSwitch is enabled.
static void	pixNxNalways(char[] pix, int x, int y, int n, java.lang.String title) pixNxNalways() - always print window of current char[] picture
static java.lang.String	pixNxNtoStr(char[] pix, int x, int y, int n, int radix, java.lang.String title) pixNxNtoStr() - convert current char[] picture of size nXn to string.
static java.lang.String	pixNxNtoStr(char[] pix, int x, int y, int n, java.lang.String title) pixNxNtoStr() - convert current char[] picture of size nXn to string.
private static java.lang.String	windmp(char[] pix, int x1, int x2, int y1, int y2, int width, java.lang.String title, int radixMode, int linesize, int maxColsToPrint, int stepSize) windmp() - Draw a window from picture 16-bit char[] 'pix' at:

Methods inherited from class Seg2Dgel.Sg2glb

get2D, get2D, getPixLineBuf, getPixLineBuf, initGlb, isDBwindow, isDBwindow, put2Dbuf, resetGlb, set2D, set2D, setPixLineBuf, setPixLineBuf, showReportStatus

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

dbugBitValues

public static int[] dbugBitValues

Debug bits values from the parsed Seg2Dgel.dbug file

dbugBitName

public static java.lang.String[] dbugBitName

Debug bits name from the parsed Seg2Dgel.dbug file

Constructor Detail

Sg2dbug

public Sg2dbug()

Sg2dbug() - Constructor

Method Detail

pixDump

public static final void pixDump(char[] pix,
                                 java.lang.String title)

pixDump() - print window of current 16-bit char[] picture if pixDumpSwitch is enabled. Displays image in [dpx1:dpx2,dpy1:dpy2] ROI.

Parameters:

pix - is the image to use

title - is the header for the output window

pixDump

public static final void pixDump(char[] pix,
                                 int radixMode,
                                 java.lang.String title)

pixDump() - print window of current 16-bit char[] picture if pixDumpSwitch is enabled. Displays image in [dpx1:dpx2,dpy1:dpy2,] ROI.

Parameters:

pix - is the image to use

radixMode - is SHOW_OCTAL, SHOW_DECIMAL, SHOW_HEX or SHOW_OD

title - is the header for the output window

dbugPixDBcode

public static final void dbugPixDBcode(char[] pix,
                                       java.lang.String title)

dbugPixDBcode() - print window of current char[] picture if enabled by dbugBitsPixFlag and (xDbug,yDbug) is inside of [dpx1:dpx2,dpy1:dpy2]. Don't print if outside of the window. Use decimal and the widthWindmp size

Parameters:

pix - is the image to use

title - is the header for the output window

dbugPixDBcode

public static final void dbugPixDBcode(char[] pix,
                                       int radixMode,
                                       java.lang.String title)

dbugPixDBcode() - print window of current char[] picture if enabled by dbugBitsPixFlag and (xDbug,yDbug) is inside of [dpx1:dpx2,dpy1:dpy2]. Don't print if outside of the window. Use decimal and the widthWindmp size

Parameters:

pix - is the image to use

radixMode - is Util.SHOW_OCTAL, SHOW_DECIMAL, SHOW_HEX or SHOW_OD

title - is the header for the output window

dbugPixNxNcode

public static final void dbugPixNxNcode(char[] pix,
                                        int x,
                                        int y,
                                        int n,
                                        java.lang.String title)

dbugPixNxNcode() - print window of size (n X n) of current char[] picture if enabled by dbugBitsPixFlag and (xDbug,yDbug) is inside of [dbx1:dbx2, dby1:dby2] to ssfFD. Don't print if outside of the window.

Parameters:

pix - is the image to use

x - is the center X of the neighborhood

y - is the center Y of the neighborhood

n - is the size of the (n X n) neighborhood (n is >=3 and is ODD!)

title - is the header for the output window

pixNxNalways

public static final void pixNxNalways(char[] pix,
                                      int x,
                                      int y,
                                      int n,
                                      java.lang.String title)

pixNxNalways() - always print window of current char[] picture

Parameters:

pix - is the image to use

x - is the center X of the neighborhood

y - is the center Y of the neighborhood

n - is the size of the (n X n) neighborhood (n is >=3 and is ODD!)

title - is the header for the output window

pixNxNtoStr

public static final java.lang.String pixNxNtoStr(char[] pix,
                                                 int x,
                                                 int y,
                                                 int n,
                                                 java.lang.String title)

pixNxNtoStr() - convert current char[] picture of size nXn to string.

Parameters:

pix - is the image to use

x - is the center X of the neighborhood

y - is the center Y of the neighborhood

n - is the size of the (n X n) neighborhood (n is >=3 and is ODD!)

title - is the header for the output window

pixNxNtoStr

public static final java.lang.String pixNxNtoStr(char[] pix,
                                                 int x,
                                                 int y,
                                                 int n,
                                                 int radix,
                                                 java.lang.String title)

pixNxNtoStr() - convert current char[] picture of size nXn to string.

Parameters:

pix - is the image to use

x - is the center X of the neighborhood

y - is the center Y of the neighborhood

n - is the size of the (n X n) neighborhood (n is >=3 and is ODD!)

title - is the header for the output window

windmp

private static final java.lang.String windmp(char[] pix,
                                             int x1,
                                             int x2,
                                             int y1,
                                             int y2,
                                             int width,
                                             java.lang.String title,
                                             int radixMode,
                                             int linesize,
                                             int maxColsToPrint,
                                             int stepSize)

windmp() - Draw a window from picture 16-bit char[] 'pix' at:

 x1,y1x2,y1
 ...
 x1,y2x2,y2.

Parameters:

pix - is image data

x1 - is left column

x2 - is right column

y1 - is top row

y2 - is bottom row

width - is the size of row

title - is title for printout

radixMode - is 0=OCTAL 1=DECIMAL 2= HEX(byte), 3= HEX(16-bits).

linesize - is Length of a line in image

maxColsToPrint - is the number of columns to print. For 80 column terminal width is 18 and 30 for a 132 column terminal.

stepSize - is pixel step size for sample/average in [1:32], 1 default

Returns:

string of window data